6M2V

Crystal structure of UHRF1 SRA complexed with fully-mCHG DNA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


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Literature

Mechanistic insights into recognition of symmetric methylated cytosines in CpG and non-CpG DNA by UHRF1 SRA.

Abhishek, S.Nakarakanti, N.K.Deeksha, W.Rajakumara, E.

(2021) Int J Biol Macromol 170: 514-522

  • DOI: 10.1016/j.ijbiomac.2020.12.149
  • Primary Citation of Related Structures:  
    6M2V

  • PubMed Abstract: 
  • Non-CpG DNA methylation (non-mCpG) is enriched in the genome of brain neurons and germline cells in mammals. Accumulation of non-mCpG during postnatal brain development correlates with gene regulation and inactivation of distal regulatory elements. R ...

    Non-CpG DNA methylation (non-mCpG) is enriched in the genome of brain neurons and germline cells in mammals. Accumulation of non-mCpG during postnatal brain development correlates with gene regulation and inactivation of distal regulatory elements. Recently, UHRF1 has been found to contribute to de novo non-CpG methylation, however, whether UHRF1 could recognize non-mCpG is unknown. Here, we have demonstrated through calorimetric measurements that the UHRF1 SRA can recognize mCpH and fully-mCpHpG, types of non-mCpG. Our ITC binding studies endorse the preferential reading of hemi-mCpG by UHRF1 SRA and also show 6-fold weaker binding for fully-mCpG than hemi-mCpG. Despite presence of symmetrical (5-methyl cytosine) 5mCs, stoichiometry of 1:1 for UHRF1 SRA binding to fully-mCpG indicates that UHRF1 SRA may not form a stable complex with fully-mCpG DNA. Contrarily, UHRF1 SRA recognizes fully-mCpHpG with a stoichiometry of 2:1 protein to DNA duplex with binding affinity higher than fully-mCpG. Our crystal structure of UHRF1 SRA bound to fully-mCpHpG DNA reveals dual flip-out mechanism of 5mC recognition. Metadynamics studies corroborates with ITC data that UHRF1 SRA could not form a stable complex with fully-mCpG DNA. Altogether, this study demonstrates that UHRF1 SRA recognizes non-mCpG DNA and exhibits contrasting mechanisms for hemi-mCpG and fully-mCpHpG DNA recognition.


    Organizational Affiliation

    Macromolecular Structural Biology Lab, Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, Telangana 502285, India. Electronic address: eraj@bt.iith.ac.in.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase UHRF1AB212Mus musculusMutation(s): 0 
Gene Names: Uhrf1Np95
EC: 2.3.2.27
Find proteins for Q8VDF2 (Mus musculus)
Explore Q8VDF2 
Go to UniProtKB:  Q8VDF2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*CP*AP*CP*GP*(5CM)P*TP*GP*CP*GP*TP*GP*A)-3')C, D13synthetic construct
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 3.00 Å
    • R-Value Free: 0.276 
    • R-Value Work: 0.234 
    • R-Value Observed: 0.236 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 55.897α = 90
    b = 74.829β = 90
    c = 141.505γ = 90
    Software Package:
    Software NamePurpose
    XDSdata reduction
    XDSdata scaling
    MOLREPphasing
    PHENIXrefinement

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Department of Biotechnology (DBT, India)India--
    Science and Engineering Research Board (SERB)India--

    Revision History 

    • Version 1.0: 2021-01-13
      Type: Initial release
    • Version 1.1: 2021-01-20
      Changes: Database references